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14 months ago
wonde2000
•
0
I run GATK4.3 for base recalibration and I got the following result. I am not sure whether my output is right or wrong. Any help is appreciated.
The warning messages are
WARN Attempting to retrieve a sequence dictionary from the associated index file
WARN IntelInflater - Zero Bytes Written : 0
WARN IndexUtils - Feature file
The first and last few lines and the last part of the result are:
Using GATK jar /export/opt/sw/gatk/4.3/gatk4_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribb le=false -Dsamjdk.compression_level=2 -jar /export/opt/sw/gatk/4.3/gatk4_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local. jar BaseRecalibrator -I ../data/Afar_rD/Afar_3_dedup.bam -R ../reference/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa --known-sites . ./GATK_reso/bos_taurus.vcf.gz --known-sites ../GATK_reso/ARS1.2PlusY_BQSR.vcf.gz -O Afar3_data.table1
16:02:11.052 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/export/opt/sw/gatk/4.3/gatk4_env/share/g atk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
16:02:11.234 INFO BaseRecalibrator - ------------------------------------------------------------
16:02:11.235 INFO BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.3.0.0
16:02:11.235 INFO BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
16:02:11.235 INFO BaseRecalibrator - Executing as wondossen@compute3.c.hgen.slu.se on Linux v3.10.0-693.21.1.el7.x86_64 amd64
16:02:11.235 INFO BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v11.0.13+7-b1751.21
16:02:11.235 INFO BaseRecalibrator - Start Date/Time: 15 February 2023 at 16:02:11 CET
16:02:11.235 INFO BaseRecalibrator - ------------------------------------------------------------
16:02:11.236 INFO BaseRecalibrator - ------------------------------------------------------------
16:02:11.237 INFO BaseRecalibrator - HTSJDK Version: 3.0.1
16:02:11.237 INFO BaseRecalibrator - Picard Version: 2.27.5
16:02:11.237 INFO BaseRecalibrator - Built for Spark Version: 2.4.5
16:02:11.237 INFO BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:02:11.237 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:02:11.237 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:02:11.237 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:02:11.237 INFO BaseRecalibrator - Deflater: IntelDeflater
16:02:11.238 INFO BaseRecalibrator - Inflater: IntelInflater
16:02:11.238 INFO BaseRecalibrator - GCS max retries/reopens: 20
16:02:11.238 INFO BaseRecalibrator - Requester pays: disabled
16:02:11.238 INFO BaseRecalibrator - Initializing engine
16:02:11.822 INFO FeatureManager - Using codec VCFCodec to read file file:///export/proj/ethiopian_cattle/NOBACKUP/../GATK_re so/bos_taurus.vcf.gz
16:02:11.979 INFO FeatureManager - Using codec VCFCodec to read file file:///export/proj/ethiopian_cattle/NOBACKUP/../GATK_re so/ARS1.2PlusY_BQSR.vcf.gz
16:02:12.092 WARN IndexUtils - Feature file "file:///export/proj/ethiopian_cattle/NOBACKUP/../GATK_reso/bos_taurus.vcf.gz" ap pears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
16:02:12.503 WARN IntelInflater - Zero Bytes Written : 0
16:02:12.506 WARN IndexUtils - Feature file "file:///export/proj/ethiopian_cattle/NOBACKUP/../GATK_reso/ARS1.2PlusY_BQSR.vcf. gz" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
16:02:12.584 WARN IntelInflater - Zero Bytes Written : 0
16:02:12.610 INFO BaseRecalibrator - Done initializing engine
16:02:12.613 INFO BaseRecalibrationEngine - The covariates being used here:
16:02:12.613 INFO BaseRecalibrationEngine - ReadGroupCovariate
16:02:12.614 INFO BaseRecalibrationEngine - QualityScoreCovariate
16:02:12.614 INFO BaseRecalibrationEngine - ContextCovariate
16:02:12.614 INFO BaseRecalibrationEngine - CycleCovariate
16:02:12.651 INFO ProgressMeter - Starting traversal
16:02:12.652 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
16:02:22.662 INFO ProgressMeter - 1:393267 0.2 258000 1546762.6
16:02:32.665 INFO ProgressMeter - 1:1606867 0.3 578000 1732960.2
16:02:42.705 INFO ProgressMeter - 1:4309110 0.5 852000 1701051.5
16:02:52.705 INFO ProgressMeter - 1:6825213 0.7 1143000 1712274.0
16:03:02.722 INFO ProgressMeter - 1:9325322 0.8 1422000 1704014.4
16:03:12.722 INFO ProgressMeter - 1:11842778 1.0 1709000 1707008.5
16:03:22.724 INFO ProgressMeter - 1:14272945 1.2 1989000 1703105.4
16:03:32.759 INFO ProgressMeter - 1:16686166 1.3 2268000 1698728.0
..
..
..
19:04:04.600 INFO ProgressMeter - NKLS02001949.1:25475 181.9 288586000 1586807.4
19:04:14.617 INFO ProgressMeter - NKLS02001029.1:14303 182.0 288865000 1586884.8
19:04:24.636 INFO ProgressMeter - NKLS02000075.1:16243 182.2 289120000 1586830.0
19:04:34.645 INFO ProgressMeter - NKLS02000522.1:15074 182.4 289396000 1586891.9
19:04:44.708 INFO ProgressMeter - NKLS02001176.1:4862 182.5 289678000 1586978.9
19:04:54.715 INFO ProgressMeter - NKLS02001731.1:1435 182.7 289951000 1587024.3
19:05:04.717 INFO ProgressMeter - NKLS02000327.1:249 182.9 290214000 1587015.8
19:05:14.722 INFO ProgressMeter - NKLS02001633.1:6427 183.0 290433000 1586766.6
19:05:24.750 INFO ProgressMeter - NKLS02001834.1:5709 183.2 290711000 1586836.3
19:05:34.762 INFO ProgressMeter - NKLS02001079.1:3182 183.4 290974000 1586826.7
19:05:44.781 INFO ProgressMeter - NKLS02000485.1:521 183.5 291289000 1587099.1
19:05:47.650 WARN IntelInflater - Zero Bytes Written : 0
19:05:47.653 INFO BaseRecalibrator - 40087222 read(s) filtered by: MappingQualityNotZeroReadFilter
0 read(s) filtered by: MappingQualityAvailableReadFilter
0 read(s) filtered by: MappedReadFilter
98300 read(s) filtered by: NotSecondaryAlignmentReadFilter
11495976 read(s) filtered by: NotDuplicateReadFilter
0 read(s) filtered by: PassesVendorQualityCheckReadFilter
0 read(s) filtered by: WellformedReadFilter
51681498 total reads filtered
19:05:47.654 INFO ProgressMeter - NKLS02001797.1:38 183.6 291356488 1587052.9
19:05:47.654 INFO ProgressMeter - Traversal complete. Processed 291356488 total reads in 183.6 minutes.
19:05:47.887 INFO BaseRecalibrator - Calculating quantized quality scores...
19:05:47.920 INFO BaseRecalibrator - Writing recalibration report...
19:05:49.708 INFO BaseRecalibrator - ...done!
19:05:49.709 INFO BaseRecalibrator - BaseRecalibrator was able to recalibrate 291356488 reads
19:05:49.709 INFO BaseRecalibrator - Shutting down engine
[15 February 2023 at 19:05:49 CET] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 183.6 5 minutes.
Runtime.totalMemory()=2579496960
Tool returned:
SUCCESS
(base)
